a quick question about picard - galaxy-dev

29 Apr 2016


      Hi All,
I wrote a very simple wrapper for one picard function. Here is the xml file:
<tool name="CreateSequenceDictionary" id="picard_CreateSequenceDictionary"
version="1.126.0">
  <description>Create Sequence Dictionary</description>
  <requirements>
    <requirement type="package" version="1.126.0">picard</requirement>
  </requirements>
<macros>
    <import>picard_macros.xml</import>
  </macros>
<command>
    @java_options@
    java -jar $JAVA_JAR_PATH/picard.jar
    CreateSequenceDictionary
    R="${ref_file}"
    O="${dict_file}"
  </command>
  <inputs>
    <param format="fa" name="ref_file" type="data" label="Using reference
genome" help="-R,--reference_sequence" />
  </inputs>
  <outputs>
    <data format="txt" name="dict_file" />
  </outputs>
  <help>
**Purpose**
Create Sequence Dictionary from fa file
  </help>
</tool>
It's ugly, I know. :-( Just want to finish a quick test...however when I
tried to run a test, it always says something like:
Exception in thread "main" picard.PicardException:
/media/4tb-ext/galaxy-data-store/database/files/008/dataset_8757.dat
already exists.  Delete this file and try again, or specify a
different output file
When I looked at that file, it has a size 0, but even I remove that
file, I'll still see the same thing.
Galaxy terminal executes:
galaxy.jobs.runners.local DEBUG 2016-04-29 13:55:51,423 (3189)
executing: GALAXY_SLOTS="1"; export GALAXY_SLOTS;
_JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} &&     export
_JAVA_OPTIONS &&               java -jar $JAVA_JAR_PATH/picard.jar
CreateSequenceDictionary
R="/media/mybook/GATK_galaxyWrapper/hg38.fa"
O="/media/4tb-ext/galaxy-data-store/database/files/008/dataset_8757.dat"
Seems it did the right thing, but why that set_meta set state to
ERROR? Oh there was indeed a warning:
WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with
extension 'eset', using datatype from
/media/4tb-ext/galaxy-data-store/database/tmp/tmp_Uuw5Y.
Have anyone seen this before? I'm quite confused since the same
commandline runs smoothly in the terminal.
Thanks,
Rui